[BioC] Recent changes to Bioconductor packages

[madman at jimmy.harvard.edu]

This is an automated message sent out weekly to report recent changes
to Bioconductor packages.  Please see the URL 
http://www.bioconductor.org/changelog.html for a complete history of 
changes.  Unless otherwise noted, these changes apply to the developmental
packages only.
-----------------------------------------------------------------------
12 September 2003: rhdf5 - Due to conflicts with 1.6.X and later of the
   HDF5 libraries, for now rhdf5 will require that the user has version
   1.4.X of the HDF5 libraries through a call in the configure script.  JG

11 September 2003: affy - the express function has been formally removed 
   (previously it was marked deprecated). ReadAffy() now calls 
   read.affybatch2() (which should be faster and have a lower memory 
   overhead). justRMA() now calls just.rma2() (which should also be 
   slightly faster and have a lower memory overhead).  BMB

10 September 2003: reposTools - when reposTools encounters a library
    which it can not write to during syncLocalLibList(), it will 
    store the appropriate locLibList structure to a temporary directory
    which will then be searched (by default) by the other functions such
    as install/update.packages2() when they are searching for installed
    versions of packages.  Previously if a directory was not writeable
    then those packages were "dead" to reposTools when the only caveat
    should be that packages can't be installed there.  JG

10 September 2003: reposTools - fixed a major bug with the way in which
    reposTools selects packages to download.  Previously reposTools would
    always select the first available pacakge from a repository if there
    were multiple versions of the same package (which always the lowest
    version number) despite this being the opposite behaviour desired, due to a 
    logic flaw in the way it constructed the package listings for
    repositories.  Likewise, some surrounding code was changed to account for 
    this as the structure itself was 'broken'. JG

09 September 2003: widgetTools - widgetTools now uses install.R JG

09 September 2003: limma 1.1.18 - new function plotDensities and new section
    in User's Guide on single channel normalization, both by Natalie Thorne. GKS